Understanding the factors driving the spread and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the local, regional, national, and international levels is important in protecting against future pandemics. By exploring their viral genomes, we attempted to analyse the spread of SARS-CoV-2 and its evolutionary convergence in Kashiwa City, as an example of a representative commuter town in Japan. From September 2020 to January 2023, a total of 47,134 nasopharyngeal swab and saliva specimens were collected from patients in 47 local clinics and hospitals, covering the vast majority of healthcare facilities. All SARS-CoV-2-positive samples were subjected to whole genome sequencing. Based on the analysis of 5,536 identified genomes, all major strains were represented. Unique regional mutations were occasionally identified in each strain. Inspection of these mutations revealed that the overall base substitution rate increased with progressive waves of the pandemic, at an overall rate of 2.56 bases/year. Interestingly, the spread and evolutionary patterns appeared to be distinct between regions and between individual clinics. Further analysis of the synonymous base substitution rate showed that the speed of viral evolution accelerated coincident with the beginning of public vaccination. Comprehensive genomic epidemiological studies, as presented here, should be useful in precisely understanding the pandemic and preparing for possible future pandemics.

中文翻译：

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SARS-CoV-2病毒基因组的进化与当地条件变化的关系：日本郊区城市的基因组流行病学研究。

了解推动严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 在地方、区域、国家和国际层面传播和演变的因素对于预防未来的流行病非常重要。通过探索病毒基因组，我们试图分析 SARS-CoV-2 的传播及其在柏市的进化趋同，作为日本代表性通勤城镇的一个例子。2020年9月至2023年1月，共采集当地47家诊所和医院患者鼻咽拭子和唾液标本47134份，覆盖绝大多数医疗机构。所有 SARS-CoV-2 阳性样本均进行了全基因组测序。基于对 5,536 个已识别基因组的分析，涵盖了所有主要菌株。每个菌株中偶尔会发现独特的区域突变。对这些突变的检查表明，总体碱基替换率随着大流行的进展而增加，总体速率为 2.56 个碱基/年。有趣的是，不同地区和各个诊所之间的传播和进化模式似乎有所不同。对同义碱基替代率的进一步分析表明，病毒进化速度随着公共疫苗接种的开始而加快。如本文所述，全面的基因组流行病学研究应该有助于准确了解这一流行病并为未来可能发生的流行病做好准备。